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Comparative network analysis reveals the dynamics of organic acid diversity during fruit ripening in peach (Prunus persica L. Batsch)

BACKGROUND: Organic acids are important components that determine the fruit flavor of peach (Prunus persica L. Batsch). However, the dynamics of organic acid diversity during fruit ripening and the key genes that modulate the organic acids metabolism remain largely unknown in this kind of fruit tree...

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Autores principales: Jiang, Xiaohan, Liu, Kangchen, Peng, Huixiang, Fang, Jing, Zhang, Aidi, Han, Yuepeng, Zhang, Xiujun
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9827700/
https://www.ncbi.nlm.nih.gov/pubmed/36617558
http://dx.doi.org/10.1186/s12870-023-04037-w
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author Jiang, Xiaohan
Liu, Kangchen
Peng, Huixiang
Fang, Jing
Zhang, Aidi
Han, Yuepeng
Zhang, Xiujun
author_facet Jiang, Xiaohan
Liu, Kangchen
Peng, Huixiang
Fang, Jing
Zhang, Aidi
Han, Yuepeng
Zhang, Xiujun
author_sort Jiang, Xiaohan
collection PubMed
description BACKGROUND: Organic acids are important components that determine the fruit flavor of peach (Prunus persica L. Batsch). However, the dynamics of organic acid diversity during fruit ripening and the key genes that modulate the organic acids metabolism remain largely unknown in this kind of fruit tree which yield ranks sixth in the world. RESULTS: In this study, we used 3D transcriptome data containing three dimensions of information, namely time, phenotype and gene expression, from 5 different varieties of peach to construct gene co-expression networks throughout fruit ripening of peach. With the network inferred, the time-ordered network comparative analysis was performed to select high-acid specific gene co-expression network and then clarify the regulatory factors controlling organic acid accumulation. As a result, network modules related to organic acid synthesis and metabolism under high-acid and low-acid comparison conditions were identified for our following research. In addition, we obtained 20 candidate genes as regulatory factors related to organic acid metabolism in peach. CONCLUSIONS: The study provides new insights into the dynamics of organic acid accumulation during fruit ripening, complements the results of classical co-expression network analysis and establishes a foundation for key genes discovery from time-series multiple species transcriptome data. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-023-04037-w.
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spelling pubmed-98277002023-01-10 Comparative network analysis reveals the dynamics of organic acid diversity during fruit ripening in peach (Prunus persica L. Batsch) Jiang, Xiaohan Liu, Kangchen Peng, Huixiang Fang, Jing Zhang, Aidi Han, Yuepeng Zhang, Xiujun BMC Plant Biol Research BACKGROUND: Organic acids are important components that determine the fruit flavor of peach (Prunus persica L. Batsch). However, the dynamics of organic acid diversity during fruit ripening and the key genes that modulate the organic acids metabolism remain largely unknown in this kind of fruit tree which yield ranks sixth in the world. RESULTS: In this study, we used 3D transcriptome data containing three dimensions of information, namely time, phenotype and gene expression, from 5 different varieties of peach to construct gene co-expression networks throughout fruit ripening of peach. With the network inferred, the time-ordered network comparative analysis was performed to select high-acid specific gene co-expression network and then clarify the regulatory factors controlling organic acid accumulation. As a result, network modules related to organic acid synthesis and metabolism under high-acid and low-acid comparison conditions were identified for our following research. In addition, we obtained 20 candidate genes as regulatory factors related to organic acid metabolism in peach. CONCLUSIONS: The study provides new insights into the dynamics of organic acid accumulation during fruit ripening, complements the results of classical co-expression network analysis and establishes a foundation for key genes discovery from time-series multiple species transcriptome data. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-023-04037-w. BioMed Central 2023-01-09 /pmc/articles/PMC9827700/ /pubmed/36617558 http://dx.doi.org/10.1186/s12870-023-04037-w Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research
Jiang, Xiaohan
Liu, Kangchen
Peng, Huixiang
Fang, Jing
Zhang, Aidi
Han, Yuepeng
Zhang, Xiujun
Comparative network analysis reveals the dynamics of organic acid diversity during fruit ripening in peach (Prunus persica L. Batsch)
title Comparative network analysis reveals the dynamics of organic acid diversity during fruit ripening in peach (Prunus persica L. Batsch)
title_full Comparative network analysis reveals the dynamics of organic acid diversity during fruit ripening in peach (Prunus persica L. Batsch)
title_fullStr Comparative network analysis reveals the dynamics of organic acid diversity during fruit ripening in peach (Prunus persica L. Batsch)
title_full_unstemmed Comparative network analysis reveals the dynamics of organic acid diversity during fruit ripening in peach (Prunus persica L. Batsch)
title_short Comparative network analysis reveals the dynamics of organic acid diversity during fruit ripening in peach (Prunus persica L. Batsch)
title_sort comparative network analysis reveals the dynamics of organic acid diversity during fruit ripening in peach (prunus persica l. batsch)
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9827700/
https://www.ncbi.nlm.nih.gov/pubmed/36617558
http://dx.doi.org/10.1186/s12870-023-04037-w
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